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Tutorial: assessing metagenomics software with the CAMI benchmarking toolkit
Nature Protocols ( IF 14.8 ) Pub Date : 2021-03-01 , DOI: 10.1038/s41596-020-00480-3
Fernando Meyer 1 , Till-Robin Lesker 1, 2 , David Koslicki 3 , Adrian Fritz 1 , Alexey Gurevich 4 , Aaron E Darling 5 , Alexander Sczyrba 6 , Andreas Bremges 1, 2 , Alice C McHardy 1
Affiliation  

Computational methods are key in microbiome research, and obtaining a quantitative and unbiased performance estimate is important for method developers and applied researchers. For meaningful comparisons between methods, to identify best practices and common use cases, and to reduce overhead in benchmarking, it is necessary to have standardized datasets, procedures and metrics for evaluation. In this tutorial, we describe emerging standards in computational meta-omics benchmarking derived and agreed upon by a larger community of researchers. Specifically, we outline recent efforts by the Critical Assessment of Metagenome Interpretation (CAMI) initiative, which supplies method developers and applied researchers with exhaustive quantitative data about software performance in realistic scenarios and organizes community-driven benchmarking challenges. We explain the most relevant evaluation metrics for assessing metagenome assembly, binning and profiling results, and provide step-by-step instructions on how to generate them. The instructions use simulated mouse gut metagenome data released in preparation for the second round of CAMI challenges and showcase the use of a repository of tool results for CAMI datasets. This tutorial will serve as a reference for the community and facilitate informative and reproducible benchmarking in microbiome research.



中文翻译:

教程:使用 CAMI 基准测试工具包评估宏基因组学软件

计算方法是微生物组研究的关键,获得定量和无偏见的性能估计对于方法开发人员和应用研究人员来说很重要。为了在方法之间进行有意义的比较,确定最佳实践和常见用例,并减少基准测试的开销,有必要使用标准化的数据集、程序和评估指标。在本教程中,我们描述了计算元组学基准测试中的新兴标准,这些标准是由更大的研究人员社区推导出来并达成一致的。具体来说,我们概述了元基因组解释的批判性评估 (CAMI) 计划最近所做的努力,该计划为方法开发人员和应用研究人员提供了有关现实场景中软件性能的详尽定量数据,并组织了社区驱动的基准测试挑战。我们解释了与评估宏基因组组装、分箱和分析结果最相关的评估指标,并提供有关如何生成它们的分步说明。这些说明使用为准备第二轮 CAMI 挑战而发布的模拟小鼠肠道宏基因组数据,并展示了 CAMI 数据集工具结果库的使用。本教程将作为社区的参考,并促进微生物组研究中信息丰富且可重复的基准测试。这些说明使用为准备第二轮 CAMI 挑战而发布的模拟小鼠肠道宏基因组数据,并展示了 CAMI 数据集工具结果库的使用。本教程将作为社区的参考,并促进微生物组研究中信息丰富且可重复的基准测试。这些说明使用为准备第二轮 CAMI 挑战而发布的模拟小鼠肠道宏基因组数据,并展示了 CAMI 数据集工具结果库的使用。本教程将作为社区的参考,并促进微生物组研究中信息丰富且可重复的基准测试。

更新日期:2021-03-01
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